A set of multi-effect endpoints and multi-level drinking water genotoxicity test system was established and applied to evaluate the drinking water treatment process in a water plant in Yancheng. Ames tester strains TA98 and TA100 were used to detect the mutagenic effects of water extracts. The micronucleus test and the comet assay of human peripheral blood lymphocyte were applied to detect chromosome breakage and DNA damage. The results of the Ames test show that mutagenicity is not observed in the range of 0.5 to 2.0 L/plate of water samples. The results of the micronucleus test exhibit that raw water, sand filter water and treated water are strong clastogenic, and can increase the lymphocyte micronucleus cell rate with the dose of 0.125 L. After the treatment with ozone and biological activated carbon, each dose has no difference with the control. The results of the comet assay show that water samples can damage DNA of lymphocyte at different doses. The effecting doses of raw water, tap water, sand filter water, and biological activated carbon(BAC)water are 0.25, 0.25, 0.50,and 1.00 L. The degree of damage from large to small is raw water, tap water, sand filter water,and BAC water.